Hox genesis

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One of the hallmark characters of animals is the presence of a specific cluster of genes that are responsible for staking out the spatial domains of the body plan along the longitudinal axis. These are the Hox genes; they are recognizable by virtue of the presence of a 60 amino acid long DNA binding region called the homeodomain, by similarities in sequence, by their role as regulatory genes expressed early in development, by the restriction of their expression to bands of tissue, by their clustering in the genome to a single location, and by the remarkable collinearity of their organization on the chromosome to their pattern of expression: the order of the gene’s position in the cluster is related to their region of expression along the length of the animal. That order has been retained in most animals (there are interesting exceptions), and has been conserved for about a billion years.

Think about that. While gene sequences have steadily changed, while chromosomes have been fractured and fused repeatedly, while differences accumulated to create forms as different as people and fruit flies and squid and sea urchins, while continents have ping-ponged about the globe and meteors have smashed into the earth and glaciers have advanced and retreated, these properties of this set of genes have remained constant. They are fundamental and crucial to basic elements of our body plan, so basic that we take them completely for granted. They determine that we can have different regions of our bodies with different organs and organization. Where did they come from and what forces constrain them to maintain their specific organization on the chromosome? Are there other genes that are comparably central to our organization?

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Bilateral symmetry in a sea anemone

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There are quite a few genes that are known to be highly conserved in both sequence and function in animals. Among these are the various Hox genes, which are expressed in an ordered pattern along the length of the organism and which define positional information along the anterior-posterior axis; and another is decapentaplegic (dpp) which is one of several conserved genes that define the dorsal-ventral axis. Together, these sets of genes establish the front-back and top-bottom axes of the animal, which in turn establishes bilaterality—this specifically laid out three-dimensional organization is a hallmark of the lineage Bilateria, to which we and 99% of all the other modern animal species belong.

There are some animals that don’t belong to the Bilateria, though: members of the phylum Cnidaria, the jellyfish, hydra, sea anemones, and corals, which are typically radially symmetric. A few cnidarian species exhibit bilateral symmetry, though, and Finnerty et al. (2004) ask a simple question: have those few species secondarily reinvented a mechanism for generating bilateral symmetry (so that this would be an example of convergent evolution), or do they use homologous mechanisms, that is, the combination of Hox genes for A-P patterning and dpp for D-V patterning? The answer is that this is almost certainly an example of homology—the same genes are being used.

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Stromatoveris

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The Cambrian vendobiont S. psygmoglena, gen.sp.nov., composite photo of part and counterpart to show both upper and lower surfaces.

From the pre-Cambrian and early Cambrian, we have a collection of enigmatic fossils: the small shellies appear to be bits and pieces of partially shelled animals; there are trace fossils, the tracks of small, soft-bodied wormlike animals; and there are the very peculiar Edicaran vendobionts, which look like fronds and fans and pleated or quilted sheets. In the Cambrian, of course, we find somewhat more familiar creatures—sure, they’re weird and different, but we can at least tentatively see them as precursors to the modern members of their respective phyla. It’s not surprising, though, that the farther back in time we go, the stranger animals appear, and the more difficult it is to place them in our phylogenies.

So here’s something cool and helpful—it looks like a vendobiont, but it’s been found in the Lower Cambrian fossil beds of Chengjiang. It’s also very well preserved, and has features that suggest affinities to the ctenophores.

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Peter Singer in Salon

These darn philosophers—how dare they make you think, even when you disagree with much of what they say? Peter Singer is one of those infuriating people who sometimes sounds so silly, but still makes a strong case.

He has an interview in Salon—if you don’t want to fuss with their ads, I’ve put an interesting excerpt below the fold. Maybe it’s time for me to get back to vegetarianism…

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Uninvention

Our Seed Overlords have asked a question (our answering is entirely voluntary, if you were wondering, and we’re only answering because it is an interesting question): “if you could cause one invention from the last hundred years never to have been made at all, which would it be, and why?“

Several of my colleagues here have coughed up answers—Adventures in Ethics and Science (with a particularly appropriate entry),

Afarensis,

Evolgen,

Living the Scientific Life, and

Stranger Fruit—but I’m going to be a little bit contrary and question the question.

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Clocks and creationists

Lisa Jardine is a historian who clearly understands how science works:

The thought uppermost in my mind was how odd it is that non-scientists think of science as being about certainties and absolute truth. Whereas scientists are actually quite tentative—they simply try to arrive at the best fit between the experimental findings so far and a general principle.

Read the rest. She ties together the ideals of how science should be carried out with a story from Pepys and an unscrupulous sea captain and modern day creationists—excellent stuff!

A brief overview of Hox genes

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In previous articles about fly development, I’d gone from the maternal gradient to genes that are expressed in alternating stripes (pair-rule genes), and mentioned some genes (the segment polarity genes) that are expressed in every segment. The end result is the development of a segmented animal: one made up of a repeated series of morphological modules, all the same.

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Building an animal with repeated elements like that is a wonderfully versatile strategy for making an organism larger without making it too much more complicated, but it’s not the whole story. Just repeating the same bits over and over again is a way to make a generic wormlike thing—a tapeworm, for instance—but even tapeworms may need to specialize certain individual segments for specific functions. At its simplest, it may be necessary to modify one end for feeding, and the opposite end for mating. So now, in addition to staking out the tissues of the embryo as belonging to discrete segments, we also need a mechanism that says “build mouthparts here (and not everywhere)”, and “put genitalia here (not over there)”.

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Naked anaspids

This strange fish is Euphanerops longaevus, which is one of two species of 370 million year old jawless fishes (the other is Endeiolepis aneri, and the paper suggests that they may actually represent differently preserved members of the same species). These are soft-bodied animals that are usually poorly preserved, and are of interest because they seem to have some properties in common with both the lampreys and the gnathostomes, or jawed fishes. Their exact position in the vertebrate family tree is problematic, and the experts go back and forth on it; sometimes they are grouped with the lampreys, sometimes as cousins more closely related to the gnathostomes.

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Euphanerops longaevus, preserved as an imprint. Scale bar, 10 mm.

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